.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data29.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 457 patterns found. (out of a total of 500 sites) . 34 sites without polymorphism (6.80%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22524.9135] [GTR parameters ] . ( 1 sec) [ -22055.3820] [Alpha ][ 0.500960] . ( 1 sec) [ -21941.2855] [ 5219] [depth= 8] . ( 1 sec) [ -21648.8817] [ 5195] [depth= 4] . ( 1 sec) [ -21264.3493] [ 5151] [depth= 1] . ( 1 sec) [ -21045.5786] [ 5122] [depth= 7] . ( 1 sec) [ -20571.2961] [ 4981] [depth= 7] . ( 1 sec) [ -20422.0734] [ 4985] [depth= 6] . ( 1 sec) [ -20180.7575] [ 4947] [depth= 11] . ( 1 sec) [ -19961.7465] [ 4934] [depth= 1] . ( 1 sec) [ -19747.9936] [ 4913] [depth= 16] . ( 1 sec) [ -19345.7512] [ 4818] [depth= 10] . ( 1 sec) [ -18978.4859] [ 4722] [depth= 15] . ( 1 sec) [ -18810.8345] [ 4685] [depth= 4] . ( 1 sec) [ -18480.5583] [ 4532] [depth= 14] . ( 1 sec) [ -18448.1205] [ 4522] [depth= 1] . ( 2 sec) [ -18324.8296] [ 4504] [depth= 2] . ( 2 sec) [ -18133.7316] [ 4439] [depth= 3] . ( 2 sec) [ -18015.5899] [ 4425] [depth= 8] . ( 2 sec) [ -17972.0339] [ 4384] [depth= 3] . ( 2 sec) [ -17858.2404] [ 4377] [depth= 1] . ( 2 sec) [ -17693.2404] [ 4371] [depth= 8] . ( 2 sec) [ -17494.7855] [ 4303] [depth= 7] . ( 2 sec) [ -17370.1858] [ 4196] [depth= 5] . ( 2 sec) [ -17263.7527] [ 4217] [depth= 1] . ( 2 sec) [ -17209.6602] [ 4196] [depth= 1] . ( 2 sec) [ -16852.9854] [ 4075] [depth= 6] . ( 2 sec) [ -16701.2430] [ 3971] [depth= 7] . ( 2 sec) [ -16688.3363] [ 3968] [depth= 1] . ( 2 sec) [ -16622.6237] [ 3973] [depth= 1] . ( 2 sec) [ -16550.0604] [ 3962] [depth= 1] . ( 2 sec) [ -16339.8220] [ 3919] [depth= 3] . ( 2 sec) [ -16189.8804] [ 3912] [depth= 2] . ( 2 sec) [ -15960.9415] [ 3863] [depth= 2] . ( 2 sec) [ -15959.9662] [ 3850] [depth= 1] . ( 2 sec) [ -15773.0575] [ 3817] [depth= 8] . ( 2 sec) [ -15756.8792] [ 3811] [depth= 1] . ( 2 sec) [ -15741.2201] [ 3826] [depth= 1] . ( 2 sec) [ -15654.4940] [ 3782] [depth= 1] . ( 3 sec) [ -15328.3540] [ 3726] [depth= 9] . ( 3 sec) [ -15270.0508] [ 3721] [depth= 1] . ( 3 sec) [ -14857.6959] [ 3607] [depth= 9] . ( 3 sec) [ -14810.6903] [ 3612] [depth= 2] . ( 3 sec) [ -14751.8063] [ 3606] [depth= 1] . ( 3 sec) [ -14640.7323] [ 3553] [depth= 4] . ( 3 sec) [ -14565.4283] [ 3519] [depth= 2] . ( 3 sec) [ -14341.4632] [ 3433] [depth= 2] . ( 3 sec) [ -13945.7542] [ 3309] [depth= 8] . ( 3 sec) [ -13865.0131] [ 3306] [depth= 2] . ( 3 sec) [ -13534.8741] [ 3242] [depth= 4] . ( 3 sec) [ -13533.6917] [ 3245] [depth= 2] . ( 3 sec) [ -13509.0617] [ 3251] [depth= 3] . ( 3 sec) [ -13347.7621] [ 3252] [depth= 2] . ( 3 sec) [ -13219.8278] [ 3184] [depth= 1] . ( 3 sec) [ -12965.3443] [ 3108] [depth= 5] . ( 3 sec) [ -12749.0823] [ 3088] [depth= 4] . ( 3 sec) [ -12608.0179] [ 3035] [depth= 1] . ( 4 sec) [ -12590.1098] [ 3020] [depth= 1] . ( 4 sec) [ -12570.4834] [ 3008] [depth= 4] . ( 4 sec) [ -12496.1327] [ 2976] [depth= 6] . ( 4 sec) [ -12395.0885] [ 2952] [depth= 7] . ( 4 sec) [ -12378.5257] [ 2961] [depth= 2] . ( 4 sec) [ -12284.3701] [ 2915] [depth= 4] . ( 4 sec) [ -12083.4103] [ 2883] [depth= 5] . ( 4 sec) [ -11674.0813] [ 2822] [depth= 10] . ( 4 sec) [ -11653.9571] [ 2811] [depth= 1] . ( 4 sec) [ -11600.7749] [ 2742] [depth= 3] . ( 4 sec) [ -11544.6185] [ 2737] [depth= 1] . ( 4 sec) [ -11540.4066] [ 2739] [depth= 1] . ( 4 sec) [ -11539.8124] [ 2744] [depth= 1] . ( 4 sec) [ -11532.6430] [ 2739] [depth= 1] . ( 4 sec) [ -11526.7450] [ 2737] [depth= 1] . ( 4 sec) [ -11446.0718] [ 2685] [depth= 3] . ( 5 sec) [ -11341.6222] [ 2661] [depth= 2] . ( 5 sec) [ -11338.7666] [ 2663] [depth= 1] . ( 5 sec) [ -11322.9834] [ 2661] [depth= 1] . ( 5 sec) [ -11311.7665] [ 2664] [depth= 1] . ( 5 sec) [ -11069.8666] [Branch lengths ] . ( 6 sec) [ -11067.1920] [GTR parameters ] . ( 6 sec) [ -11021.4465] [Alpha ][ 0.961270] . ( 6 sec) [ -11018.0060] [ 2666] [depth= 1] . ( 6 sec) [ -11017.5152] [ 2669] [depth= 1] . ( 6 sec) [ -11012.7540] [ 2666] [depth= 1] . ( 6 sec) [ -10997.6445] [ 2650] [depth= 1] . ( 6 sec) [ -10997.1798] [ 2643] [depth= 1] . ( 6 sec) [ -10996.8751] [ 2640] [depth= 1] . ( 7 sec) [ -10987.6733] [ 2641] [depth= 2] . ( 7 sec) [ -10987.2345] [ 2639] [depth= 1] . ( 7 sec) [ -10979.2829] [ 2640] [depth= 1] . ( 7 sec) [ -10975.1274] [ 2635] [depth= 1] . ( 7 sec) [ -10973.2258] [ 2637] [depth= 1] . ( 7 sec) [ -10869.5588] [ 2581] [depth= 1] . ( 8 sec) [ -10849.1404] [ 2579] [depth= 1] . ( 8 sec) [ -10846.8285] [ 2581] [depth= 1] . ( 8 sec) [ -10845.1231] [ 2578] [depth= 2] . ( 8 sec) [ -10844.5302] [ 2582] [depth= 1] . ( 8 sec) [ -10844.3117] [ 2585] [depth= 1] . ( 8 sec) [ -10844.0865] [ 2582] [depth= 1] . ( 9 sec) [ -10843.9104] [ 2587] [depth= 1] . ( 9 sec) [ -10841.6240] [ 2593] [depth= 1] . ( 9 sec) [ -10840.2422] [ 2594] [depth= 1] . ( 10 sec) [ -10811.5247] [Branch lengths ] . ( 10 sec) [ -10811.4296] [GTR parameters ] . ( 10 sec) [ -10809.2404] [Alpha ][ 1.108894] . ( 10 sec) [ -10809.1804] [ 2591] [depth= 1] . ( 11 sec) [ -10807.3650] [ 2591] [depth= 1] . ( 12 sec) [ -10806.6631] [ 2593] [depth= 1] . ( 12 sec) [ -10806.2174] [ 2592] [depth= 1] . ( 13 sec) [ -10806.2035] [ 2590] [depth= 1] . ( 14 sec) [ -10802.9990] [Branch lengths ] . ( 14 sec) [ -10802.9855] [GTR parameters ] . ( 14 sec) [ -10802.9023] [Alpha ][ 1.139997] . ( 15 sec) [ -10802.4901] [ 2588] [depth= 1] . ( 16 sec) [ -10802.4131] [ 2580] [depth= 1] . ( 18 sec) [ -10801.3661] [Branch lengths ] . ( 18 sec) [ -10801.3644] [GTR parameters ] . ( 18 sec) [ -10801.3641] [Alpha ][ 1.141864] . ( 18 sec) [ -10801.3086] [ 2583] [depth= 1] . ( 21 sec) [ -10801.0927] [Branch lengths ] . ( 21 sec) [ -10801.0924] [GTR parameters ] . ( 21 sec) [ -10801.0923] [Alpha ][ 1.143006] . ( 43 sec) [ -10801.0384] [Branch lengths ] . ( 43 sec) [ -10801.0384] [Topology ] . ( 44 sec) [ -10800.8016] [Topology ] . ( 45 sec) [ -10800.7426] [Topology ] . ( 46 sec) [ -10800.7286] [Topology ] . ( 47 sec) [ -10800.7235] [Topology ] . ( 48 sec) [ -10800.7216] [Topology ] . ( 48 sec) [ -10800.7208] [Topology ] . ( 49 sec) [ -10800.7195] [GTR parameters ] . ( 49 sec) [ -10800.7195] [Alpha ][ 1.141863] . ( 49 sec) [ -10800.7195] [Topology ] . ( 49 sec) [ -10800.7191] [Topology ] . ( 50 sec) [ -10800.7190] [GTR parameters ] . ( 50 sec) [ -10800.7190] [Alpha ][ 1.141863] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10800.719026. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22110.4824] [GTR parameters ] . ( 1 sec) [ -21718.2901] [Alpha ][ 0.500960] . ( 1 sec) [ -21573.6938] [ 5179] [depth= 3] . ( 1 sec) [ -21344.1065] [ 5151] [depth= 10] . ( 1 sec) [ -21179.6053] [ 5125] [depth= 3] . ( 1 sec) [ -21095.2164] [ 5093] [depth= 7] . ( 1 sec) [ -20925.7818] [ 5026] [depth= 4] . ( 1 sec) [ -20813.5129] [ 5047] [depth= 8] . ( 1 sec) [ -20784.8850] [ 5051] [depth= 1] . ( 1 sec) [ -20640.2043] [ 5038] [depth= 5] . ( 1 sec) [ -20475.1611] [ 4997] [depth= 2] . ( 1 sec) [ -20441.0247] [ 4983] [depth= 3] . ( 1 sec) [ -20153.8392] [ 4899] [depth= 3] . ( 1 sec) [ -19822.9584] [ 4893] [depth= 7] . ( 1 sec) [ -19676.1797] [ 4764] [depth= 2] . ( 1 sec) [ -19475.1350] [ 4741] [depth= 2] . ( 1 sec) [ -18960.0291] [ 4582] [depth= 10] . ( 1 sec) [ -18746.1315] [ 4539] [depth= 8] . ( 1 sec) [ -18624.9171] [ 4468] [depth= 14] . ( 1 sec) [ -18557.1421] [ 4465] [depth= 1] . ( 1 sec) [ -18338.0179] [ 4475] [depth= 1] . ( 1 sec) [ -18307.0110] [ 4424] [depth= 1] . ( 1 sec) [ -18029.8426] [ 4355] [depth= 4] . ( 2 sec) [ -17752.1249] [ 4246] [depth= 4] . ( 2 sec) [ -17532.4908] [ 4231] [depth= 4] . ( 2 sec) [ -17486.8437] [ 4227] [depth= 6] . ( 2 sec) [ -17447.0998] [ 4221] [depth= 5] . ( 2 sec) [ -17357.2103] [ 4213] [depth= 2] . ( 2 sec) [ -17161.6142] [ 4140] [depth= 7] . ( 2 sec) [ -16467.3177] [ 4003] [depth= 7] . ( 2 sec) [ -16402.4501] [ 4018] [depth= 4] . ( 2 sec) [ -15633.5848] [ 3822] [depth= 9] . ( 2 sec) [ -15408.3122] [ 3699] [depth= 9] . ( 2 sec) [ -15258.9780] [ 3632] [depth= 3] . ( 2 sec) [ -14869.7667] [ 3535] [depth= 3] . ( 2 sec) [ -14791.7522] [ 3514] [depth= 1] . ( 2 sec) [ -14751.3184] [ 3506] [depth= 1] . ( 2 sec) [ -14640.8417] [ 3441] [depth= 6] . ( 2 sec) [ -14581.2700] [ 3433] [depth= 5] . ( 2 sec) [ -14357.0876] [ 3448] [depth= 10] . ( 2 sec) [ -14260.8081] [ 3404] [depth= 1] . ( 3 sec) [ -14123.1491] [ 3367] [depth= 3] . ( 3 sec) [ -13837.6915] [ 3273] [depth= 5] . ( 3 sec) [ -13670.3446] [ 3236] [depth= 8] . ( 3 sec) [ -13460.7434] [ 3150] [depth= 10] . ( 3 sec) [ -13418.7754] [ 3151] [depth= 4] . ( 3 sec) [ -13382.9910] [ 3131] [depth= 1] . ( 3 sec) [ -12992.6415] [ 3030] [depth= 6] . ( 3 sec) [ -12971.9686] [ 3031] [depth= 3] . ( 3 sec) [ -12652.6280] [ 3033] [depth= 11] . ( 3 sec) [ -12643.5511] [ 3027] [depth= 4] . ( 3 sec) [ -12566.4972] [ 3012] [depth= 1] . ( 3 sec) [ -12470.7414] [ 2971] [depth= 4] . ( 3 sec) [ -12435.5783] [ 2966] [depth= 1] . ( 3 sec) [ -12426.8649] [ 2960] [depth= 2] . ( 3 sec) [ -12417.5281] [ 2969] [depth= 2] . ( 3 sec) [ -12300.1438] [ 2921] [depth= 1] . ( 3 sec) [ -12093.2325] [ 2851] [depth= 3] . ( 3 sec) [ -12063.6153] [ 2862] [depth= 1] . ( 4 sec) [ -12014.3718] [ 2848] [depth= 1] . ( 4 sec) [ -11981.7352] [ 2838] [depth= 1] . ( 4 sec) [ -11980.2234] [ 2847] [depth= 1] . ( 4 sec) [ -11911.0739] [ 2881] [depth= 1] . ( 4 sec) [ -11903.3399] [ 2883] [depth= 1] . ( 4 sec) [ -11892.5867] [ 2877] [depth= 1] . ( 4 sec) [ -11638.6028] [ 2837] [depth= 2] . ( 4 sec) [ -11455.8553] [ 2751] [depth= 5] . ( 4 sec) [ -11453.5816] [ 2755] [depth= 1] . ( 4 sec) [ -11423.8984] [ 2715] [depth= 4] . ( 4 sec) [ -11409.8018] [ 2719] [depth= 1] . ( 4 sec) [ -11400.1708] [ 2710] [depth= 1] . ( 4 sec) [ -11397.4902] [ 2707] [depth= 1] . ( 5 sec) [ -11169.7722] [Branch lengths ] . ( 6 sec) [ -11167.2114] [GTR parameters ] . ( 6 sec) [ -11125.2975] [Alpha ][ 0.936667] . ( 6 sec) [ -11108.0534] [ 2678] [depth= 2] . ( 6 sec) [ -11104.3279] [ 2680] [depth= 2] . ( 6 sec) [ -11100.0333] [ 2683] [depth= 1] . ( 6 sec) [ -11098.9767] [ 2685] [depth= 1] . ( 6 sec) [ -11097.3665] [ 2685] [depth= 1] . ( 6 sec) [ -11096.5861] [ 2688] [depth= 1] . ( 6 sec) [ -11091.4813] [ 2683] [depth= 4] . ( 6 sec) [ -10957.0504] [ 2598] [depth= 3] . ( 6 sec) [ -10953.3713] [ 2607] [depth= 1] . ( 6 sec) [ -10951.3621] [ 2607] [depth= 1] . ( 6 sec) [ -10924.6389] [ 2594] [depth= 1] . ( 7 sec) [ -10922.4573] [ 2579] [depth= 2] . ( 7 sec) [ -10862.3960] [ 2579] [depth= 1] . ( 7 sec) [ -10861.1952] [ 2589] [depth= 3] . ( 7 sec) [ -10859.6310] [ 2588] [depth= 1] . ( 7 sec) [ -10859.2108] [ 2592] [depth= 1] . ( 8 sec) [ -10856.2782] [ 2576] [depth= 3] . ( 8 sec) [ -10852.2672] [ 2590] [depth= 1] . ( 8 sec) [ -10851.9651] [ 2595] [depth= 1] . ( 8 sec) [ -10850.9612] [ 2606] [depth= 1] . ( 8 sec) [ -10850.4414] [ 2603] [depth= 1] . ( 9 sec) [ -10846.4283] [ 2610] [depth= 1] . ( 9 sec) [ -10825.2899] [Branch lengths ] . ( 9 sec) [ -10825.0124] [GTR parameters ] . ( 10 sec) [ -10821.8849] [Alpha ][ 1.113448] . ( 10 sec) [ -10821.8389] [ 2611] [depth= 1] . ( 10 sec) [ -10821.2775] [ 2608] [depth= 1] . ( 11 sec) [ -10812.4694] [ 2605] [depth= 2] . ( 12 sec) [ -10807.6251] [ 2606] [depth= 1] . ( 12 sec) [ -10806.2809] [ 2610] [depth= 1] . ( 12 sec) [ -10805.8023] [ 2612] [depth= 1] . ( 12 sec) [ -10805.6861] [ 2609] [depth= 1] . ( 14 sec) [ -10805.5458] [ 2608] [depth= 1] . ( 14 sec) [ -10802.4541] [Branch lengths ] . ( 14 sec) [ -10802.3958] [GTR parameters ] . ( 15 sec) [ -10802.3256] [Alpha ][ 1.142194] . ( 15 sec) [ -10802.2566] [ 2610] [depth= 1] . ( 15 sec) [ -10802.2121] [ 2609] [depth= 1] . ( 17 sec) [ -10802.1854] [ 2608] [depth= 1] . ( 18 sec) [ -10802.0791] [ 2604] [depth= 1] . ( 19 sec) [ -10801.5439] [Branch lengths ] . ( 19 sec) [ -10801.5437] [GTR parameters ] . ( 19 sec) [ -10801.5437] [Alpha ][ 1.143337] . ( 20 sec) [ -10801.3646] [ 2599] [depth= 1] . ( 41 sec) [ -10801.1757] [Branch lengths ] . ( 41 sec) [ -10801.1755] [GTR parameters ] . ( 41 sec) [ -10801.1752] [Alpha ][ 1.141172] . ( 41 sec) [ -10801.1752] [Topology ] . ( 42 sec) [ -10800.9057] [Topology ] . ( 43 sec) [ -10800.8385] [Topology ] . ( 44 sec) [ -10800.8208] [Topology ] . ( 45 sec) [ -10800.8140] [Topology ] . ( 46 sec) [ -10800.8111] [Topology ] . ( 46 sec) [ -10800.8098] [Topology ] . ( 47 sec) [ -10800.8093] [Topology ] . ( 48 sec) [ -10800.8083] [GTR parameters ] . ( 48 sec) [ -10800.8082] [Alpha ][ 1.139870] . ( 48 sec) [ -10800.8082] [Topology ] . ( 48 sec) [ -10800.8079] [Topology ] . ( 49 sec) [ -10800.8078] [GTR parameters ] . ( 49 sec) [ -10800.8078] [Alpha ][ 1.139870] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10800.807824. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22849.3480] [GTR parameters ] . ( 1 sec) [ -22411.4923] [Alpha ][ 0.500960] . ( 1 sec) [ -22062.9062] [ 5309] [depth= 8] . ( 1 sec) [ -21672.0830] [ 5302] [depth= 11] . ( 1 sec) [ -21566.4521] [ 5287] [depth= 4] . ( 1 sec) [ -21487.0210] [ 5280] [depth= 4] . ( 1 sec) [ -21276.9043] [ 5240] [depth= 9] . ( 1 sec) [ -20961.8018] [ 5238] [depth= 2] . ( 1 sec) [ -20340.2342] [ 5084] [depth= 14] . ( 1 sec) [ -20032.1838] [ 5035] [depth= 9] . ( 1 sec) [ -19633.8426] [ 4991] [depth= 9] . ( 1 sec) [ -19535.8016] [ 4997] [depth= 5] . ( 1 sec) [ -19299.9053] [ 4907] [depth= 6] . ( 1 sec) [ -19270.0072] [ 4879] [depth= 11] . ( 1 sec) [ -18777.8542] [ 4812] [depth= 1] . ( 2 sec) [ -18716.7268] [ 4806] [depth= 1] . ( 2 sec) [ -18654.0607] [ 4715] [depth= 8] . ( 2 sec) [ -18650.0592] [ 4716] [depth= 2] . ( 2 sec) [ -18625.2940] [ 4709] [depth= 4] . ( 2 sec) [ -18559.8448] [ 4698] [depth= 1] . ( 2 sec) [ -18438.1544] [ 4703] [depth= 1] . ( 2 sec) [ -18200.5273] [ 4649] [depth= 10] . ( 2 sec) [ -18089.7185] [ 4600] [depth= 1] . ( 2 sec) [ -17830.0953] [ 4482] [depth= 8] . ( 2 sec) [ -17752.3641] [ 4465] [depth= 1] . ( 2 sec) [ -17735.1355] [ 4460] [depth= 1] . ( 2 sec) [ -17241.7482] [ 4346] [depth= 10] . ( 2 sec) [ -16982.9594] [ 4343] [depth= 1] . ( 2 sec) [ -16971.6688] [ 4280] [depth= 9] . ( 2 sec) [ -16953.8038] [ 4277] [depth= 10] . ( 2 sec) [ -16938.8560] [ 4201] [depth= 1] . ( 2 sec) [ -16595.2465] [ 4102] [depth= 8] . ( 2 sec) [ -16227.1421] [ 4026] [depth= 4] . ( 2 sec) [ -16224.9026] [ 4036] [depth= 1] . ( 2 sec) [ -15945.2714] [ 3977] [depth= 9] . ( 3 sec) [ -15726.4475] [ 3864] [depth= 8] . ( 3 sec) [ -15189.8218] [ 3859] [depth= 1] . ( 3 sec) [ -15184.4686] [ 3820] [depth= 7] . ( 3 sec) [ -15144.2737] [ 3762] [depth= 7] . ( 3 sec) [ -14829.9926] [ 3761] [depth= 5] . ( 3 sec) [ -14422.4765] [ 3610] [depth= 10] . ( 3 sec) [ -14346.4714] [ 3572] [depth= 8] . ( 3 sec) [ -14169.9640] [ 3577] [depth= 7] . ( 3 sec) [ -14108.6207] [ 3586] [depth= 8] . ( 3 sec) [ -14056.3850] [ 3575] [depth= 1] . ( 3 sec) [ -14005.0766] [ 3575] [depth= 1] . ( 3 sec) [ -13936.4936] [ 3550] [depth= 1] . ( 3 sec) [ -13922.2575] [ 3550] [depth= 2] . ( 3 sec) [ -13791.5459] [ 3533] [depth= 2] . ( 3 sec) [ -13589.0513] [ 3492] [depth= 1] . ( 3 sec) [ -13525.3332] [ 3479] [depth= 3] . ( 3 sec) [ -13358.3810] [ 3425] [depth= 5] . ( 3 sec) [ -13205.0357] [ 3438] [depth= 1] . ( 4 sec) [ -12956.3431] [ 3298] [depth= 4] . ( 4 sec) [ -12936.7646] [ 3279] [depth= 8] . ( 4 sec) [ -12911.1657] [ 3238] [depth= 1] . ( 4 sec) [ -12685.0375] [ 3190] [depth= 7] . ( 4 sec) [ -12683.1825] [ 3194] [depth= 1] . ( 4 sec) [ -12532.3464] [ 3123] [depth= 5] . ( 4 sec) [ -12348.1823] [ 3030] [depth= 6] . ( 4 sec) [ -12347.0439] [ 3037] [depth= 1] . ( 4 sec) [ -12346.7589] [ 3033] [depth= 1] . ( 4 sec) [ -12238.5834] [ 3020] [depth= 7] . ( 4 sec) [ -12213.9333] [ 3013] [depth= 1] . ( 4 sec) [ -12177.9041] [ 3007] [depth= 1] . ( 4 sec) [ -12174.7719] [ 3038] [depth= 7] . ( 4 sec) [ -12079.2676] [ 3033] [depth= 1] . ( 4 sec) [ -12071.3983] [ 3034] [depth= 2] . ( 4 sec) [ -11939.7121] [ 2961] [depth= 5] . ( 4 sec) [ -11909.8741] [ 2959] [depth= 1] . ( 5 sec) [ -11893.5579] [ 2952] [depth= 2] . ( 5 sec) [ -11776.8857] [ 2921] [depth= 5] . ( 5 sec) [ -11713.5949] [ 2882] [depth= 2] . ( 5 sec) [ -11610.0917] [ 2823] [depth= 2] . ( 5 sec) [ -11551.3046] [ 2794] [depth= 6] . ( 5 sec) [ -11418.8863] [ 2753] [depth= 3] . ( 5 sec) [ -11398.6842] [ 2766] [depth= 2] . ( 5 sec) [ -11390.6102] [ 2757] [depth= 1] . ( 5 sec) [ -11335.9809] [ 2756] [depth= 3] . ( 5 sec) [ -11109.7144] [Branch lengths ] . ( 6 sec) [ -11108.1641] [GTR parameters ] . ( 6 sec) [ -11052.8372] [Alpha ][ 0.977033] . ( 6 sec) [ -11016.2444] [ 2692] [depth= 8] . ( 6 sec) [ -11014.5047] [ 2694] [depth= 1] . ( 6 sec) [ -11004.2090] [ 2683] [depth= 2] . ( 6 sec) [ -10943.4641] [ 2634] [depth= 5] . ( 6 sec) [ -10942.5015] [ 2625] [depth= 2] . ( 7 sec) [ -10941.7220] [ 2622] [depth= 1] . ( 7 sec) [ -10899.5840] [ 2600] [depth= 2] . ( 7 sec) [ -10883.2257] [ 2584] [depth= 1] . ( 7 sec) [ -10877.4662] [ 2569] [depth= 1] . ( 7 sec) [ -10871.9507] [ 2569] [depth= 1] . ( 7 sec) [ -10869.5297] [ 2566] [depth= 1] . ( 7 sec) [ -10859.4828] [ 2572] [depth= 3] . ( 7 sec) [ -10853.1078] [ 2573] [depth= 1] . ( 7 sec) [ -10848.8523] [ 2589] [depth= 1] . ( 8 sec) [ -10848.2192] [ 2589] [depth= 1] . ( 8 sec) [ -10847.7144] [ 2588] [depth= 1] . ( 8 sec) [ -10846.8099] [ 2589] [depth= 1] . ( 8 sec) [ -10835.5129] [ 2578] [depth= 1] . ( 9 sec) [ -10833.8360] [ 2582] [depth= 1] . ( 9 sec) [ -10808.2944] [Branch lengths ] . ( 10 sec) [ -10807.5075] [GTR parameters ] . ( 10 sec) [ -10805.2986] [Alpha ][ 1.125115] . ( 11 sec) [ -10804.6496] [ 2579] [depth= 1] . ( 13 sec) [ -10804.5817] [ 2584] [depth= 1] . ( 13 sec) [ -10801.9257] [Branch lengths ] . ( 13 sec) [ -10801.9216] [GTR parameters ] . ( 13 sec) [ -10801.9036] [Alpha ][ 1.140023] . ( 17 sec) [ -10801.3247] [Branch lengths ] . ( 39 sec) [ -10801.2471] [Branch lengths ] . ( 39 sec) [ -10801.2471] [Topology ] . ( 40 sec) [ -10801.2379] [Topology ] . ( 40 sec) [ -10801.2346] [Topology ] . ( 41 sec) [ -10801.2330] [Topology ] . ( 42 sec) [ -10801.2322] [Topology ] . ( 42 sec) [ -10801.2312] [GTR parameters ] . ( 42 sec) [ -10801.2312] [Alpha ][ 1.141163] . ( 42 sec) [ -10801.2312] [Topology ] . ( 43 sec) [ -10801.2307] [Topology ] . ( 43 sec) [ -10801.2307] [GTR parameters ] . ( 43 sec) [ -10801.2307] [Alpha ][ 1.141163] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -10800.8929] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -10800.7318] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10800.731776. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22642.1818] [GTR parameters ] . ( 1 sec) [ -22197.1514] [Alpha ][ 0.500960] . ( 1 sec) [ -22049.0517] [ 5166] [depth= 8] . ( 1 sec) [ -21889.2678] [ 5124] [depth= 4] . ( 1 sec) [ -21438.5338] [ 5040] [depth= 8] . ( 1 sec) [ -21376.6435] [ 5026] [depth= 1] . ( 1 sec) [ -21061.9108] [ 4995] [depth= 9] . ( 1 sec) [ -20830.5823] [ 4978] [depth= 2] . ( 1 sec) [ -20721.5561] [ 4965] [depth= 6] . ( 1 sec) [ -20518.0680] [ 4890] [depth= 5] . ( 1 sec) [ -20275.4394] [ 4866] [depth= 4] . ( 1 sec) [ -20150.7325] [ 4862] [depth= 11] . ( 2 sec) [ -19807.1595] [ 4732] [depth= 11] . ( 2 sec) [ -19679.1425] [ 4693] [depth= 7] . ( 2 sec) [ -19446.8646] [ 4671] [depth= 1] . ( 2 sec) [ -19041.0863] [ 4629] [depth= 2] . ( 2 sec) [ -18948.0343] [ 4631] [depth= 5] . ( 2 sec) [ -18548.4766] [ 4449] [depth= 6] . ( 2 sec) [ -18316.1564] [ 4377] [depth= 4] . ( 2 sec) [ -18282.0573] [ 4375] [depth= 2] . ( 2 sec) [ -18000.4277] [ 4357] [depth= 3] . ( 2 sec) [ -17656.2659] [ 4329] [depth= 10] . ( 2 sec) [ -17624.7415] [ 4323] [depth= 14] . ( 2 sec) [ -17510.8412] [ 4267] [depth= 4] . ( 2 sec) [ -17284.7782] [ 4196] [depth= 7] . ( 2 sec) [ -16716.8257] [ 4077] [depth= 14] . ( 2 sec) [ -16464.3100] [ 3979] [depth= 13] . ( 2 sec) [ -15914.3287] [ 3890] [depth= 17] . ( 2 sec) [ -15753.2108] [ 3857] [depth= 15] . ( 2 sec) [ -15697.4462] [ 3810] [depth= 1] . ( 2 sec) [ -15684.1198] [ 3820] [depth= 1] . ( 3 sec) [ -15681.0406] [ 3810] [depth= 1] . ( 3 sec) [ -15601.8010] [ 3767] [depth= 11] . ( 3 sec) [ -15258.9656] [ 3615] [depth= 6] . ( 3 sec) [ -15200.4076] [ 3604] [depth= 1] . ( 3 sec) [ -15103.4391] [ 3558] [depth= 1] . ( 3 sec) [ -14771.9143] [ 3496] [depth= 3] . ( 3 sec) [ -14757.6230] [ 3505] [depth= 1] . ( 3 sec) [ -14583.2994] [ 3425] [depth= 4] . ( 3 sec) [ -14538.1203] [ 3419] [depth= 1] . ( 3 sec) [ -14416.4091] [ 3404] [depth= 1] . ( 3 sec) [ -14298.0101] [ 3364] [depth= 7] . ( 3 sec) [ -14265.7162] [ 3357] [depth= 1] . ( 3 sec) [ -14234.7359] [ 3340] [depth= 1] . ( 3 sec) [ -13580.2348] [ 3280] [depth= 8] . ( 3 sec) [ -13545.0757] [ 3266] [depth= 1] . ( 3 sec) [ -13440.7448] [ 3214] [depth= 2] . ( 3 sec) [ -13429.2433] [ 3210] [depth= 2] . ( 3 sec) [ -13332.3017] [ 3104] [depth= 11] . ( 3 sec) [ -12790.8692] [ 3010] [depth= 10] . ( 3 sec) [ -12733.5569] [ 3014] [depth= 1] . ( 3 sec) [ -12723.1612] [ 3026] [depth= 3] . ( 4 sec) [ -12645.3966] [ 3019] [depth= 4] . ( 4 sec) [ -12609.4703] [ 3026] [depth= 1] . ( 4 sec) [ -12538.6794] [ 3026] [depth= 1] . ( 4 sec) [ -12524.6524] [ 3025] [depth= 2] . ( 4 sec) [ -12105.0765] [ 2970] [depth= 7] . ( 4 sec) [ -12058.0574] [ 2963] [depth= 1] . ( 4 sec) [ -12045.9209] [ 2964] [depth= 2] . ( 4 sec) [ -11706.3778] [ 2890] [depth= 5] . ( 4 sec) [ -11697.8964] [ 2874] [depth= 2] . ( 4 sec) [ -11674.3512] [ 2853] [depth= 4] . ( 4 sec) [ -11599.1533] [ 2842] [depth= 4] . ( 4 sec) [ -11571.2792] [ 2829] [depth= 1] . ( 4 sec) [ -11552.2424] [ 2826] [depth= 6] . ( 4 sec) [ -11445.2904] [ 2738] [depth= 5] . ( 4 sec) [ -11434.5289] [ 2747] [depth= 1] . ( 4 sec) [ -11425.2060] [ 2747] [depth= 2] . ( 4 sec) [ -11324.2378] [ 2687] [depth= 3] . ( 5 sec) [ -11320.2002] [ 2690] [depth= 1] . ( 5 sec) [ -11238.5156] [ 2646] [depth= 5] . ( 5 sec) [ -11221.8504] [ 2643] [depth= 1] . ( 5 sec) [ -11207.7871] [ 2631] [depth= 5] . ( 5 sec) [ -11204.0093] [ 2629] [depth= 1] . ( 5 sec) [ -11192.7581] [ 2637] [depth= 6] . ( 5 sec) [ -11183.0673] [ 2634] [depth= 2] . ( 5 sec) [ -11166.4289] [ 2639] [depth= 2] . ( 5 sec) [ -10975.9729] [Branch lengths ] . ( 6 sec) [ -10973.5230] [GTR parameters ] . ( 6 sec) [ -10923.6483] [Alpha ][ 0.994199] . ( 6 sec) [ -10923.1285] [ 2635] [depth= 3] . ( 6 sec) [ -10922.2219] [ 2633] [depth= 1] . ( 6 sec) [ -10912.5916] [ 2627] [depth= 4] . ( 7 sec) [ -10911.3602] [ 2629] [depth= 1] . ( 7 sec) [ -10911.1344] [ 2627] [depth= 1] . ( 7 sec) [ -10877.2399] [ 2600] [depth= 3] . ( 7 sec) [ -10867.3961] [ 2598] [depth= 2] . ( 7 sec) [ -10862.7215] [ 2590] [depth= 2] . ( 7 sec) [ -10847.1176] [ 2577] [depth= 1] . ( 7 sec) [ -10843.5308] [ 2580] [depth= 1] . ( 7 sec) [ -10842.8004] [ 2580] [depth= 1] . ( 7 sec) [ -10842.2808] [ 2577] [depth= 1] . ( 8 sec) [ -10837.5285] [ 2573] [depth= 1] . ( 8 sec) [ -10837.3336] [ 2578] [depth= 1] . ( 8 sec) [ -10837.1826] [ 2579] [depth= 1] . ( 8 sec) [ -10835.9617] [ 2582] [depth= 1] . ( 9 sec) [ -10835.7822] [ 2586] [depth= 1] . ( 9 sec) [ -10835.3694] [ 2590] [depth= 1] . ( 9 sec) [ -10834.6743] [ 2586] [depth= 1] . ( 9 sec) [ -10834.5046] [ 2594] [depth= 1] . ( 10 sec) [ -10820.9963] [Branch lengths ] . ( 10 sec) [ -10820.6936] [GTR parameters ] . ( 10 sec) [ -10819.0799] [Alpha ][ 1.126102] . ( 11 sec) [ -10818.9701] [ 2594] [depth= 1] . ( 11 sec) [ -10818.9115] [ 2586] [depth= 1] . ( 12 sec) [ -10818.7418] [ 2583] [depth= 1] . ( 12 sec) [ -10815.0819] [ 2588] [depth= 1] . ( 13 sec) [ -10807.5349] [ 2584] [depth= 1] . ( 13 sec) [ -10805.9729] [ 2588] [depth= 1] . ( 13 sec) [ -10805.5321] [ 2580] [depth= 1] . ( 14 sec) [ -10801.3207] [Branch lengths ] . ( 15 sec) [ -10801.2998] [GTR parameters ] . ( 15 sec) [ -10801.2751] [Alpha ][ 1.143854] . ( 18 sec) [ -10800.7822] [Branch lengths ] . ( 40 sec) [ -10800.7314] [Branch lengths ] . ( 40 sec) [ -10800.7314] [Topology ] . ( 41 sec) [ -10800.7250] [Topology ] . ( 41 sec) [ -10800.7224] [Topology ] . ( 42 sec) [ -10800.7211] [Topology ] . ( 43 sec) [ -10800.7205] [Topology ] . ( 44 sec) [ -10800.7198] [GTR parameters ] . ( 44 sec) [ -10800.7196] [Alpha ][ 1.142148] . ( 44 sec) [ -10800.7196] [Topology ] . ( 45 sec) [ -10800.7192] [Topology ] . ( 45 sec) [ -10800.7192] [GTR parameters ] . ( 45 sec) [ -10800.7192] [Alpha ][ 1.142148] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10800.719169. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22263.1466] [GTR parameters ] . ( 1 sec) [ -21831.2994] [Alpha ][ 0.500960] . ( 1 sec) [ -21531.6380] [ 5384] [depth= 6] . ( 1 sec) [ -21331.5569] [ 5359] [depth= 8] . ( 1 sec) [ -21254.2729] [ 5314] [depth= 6] . ( 1 sec) [ -21089.0980] [ 5301] [depth= 1] . ( 1 sec) [ -20939.8771] [ 5200] [depth= 4] . ( 1 sec) [ -20880.3920] [ 5189] [depth= 3] . ( 1 sec) [ -20742.6185] [ 5192] [depth= 6] . ( 1 sec) [ -20663.6348] [ 5183] [depth= 11] . ( 1 sec) [ -20417.6919] [ 5053] [depth= 19] . ( 1 sec) [ -20067.5286] [ 4915] [depth= 8] . ( 1 sec) [ -19992.4975] [ 4910] [depth= 2] . ( 1 sec) [ -19786.0079] [ 4843] [depth= 17] . ( 1 sec) [ -19543.6614] [ 4866] [depth= 17] . ( 1 sec) [ -19497.7215] [ 4872] [depth= 1] . ( 2 sec) [ -18967.3646] [ 4739] [depth= 11] . ( 2 sec) [ -18712.1901] [ 4718] [depth= 5] . ( 2 sec) [ -18697.7316] [ 4714] [depth= 2] . ( 2 sec) [ -18675.5691] [ 4708] [depth= 1] . ( 2 sec) [ -18546.5721] [ 4680] [depth= 14] . ( 2 sec) [ -18185.0839] [ 4582] [depth= 10] . ( 2 sec) [ -18148.9662] [ 4566] [depth= 1] . ( 2 sec) [ -17394.0458] [ 4446] [depth= 10] . ( 2 sec) [ -17351.3340] [ 4448] [depth= 1] . ( 2 sec) [ -17065.6221] [ 4378] [depth= 10] . ( 2 sec) [ -16975.3123] [ 4358] [depth= 2] . ( 2 sec) [ -16621.9779] [ 4250] [depth= 9] . ( 2 sec) [ -16541.9307] [ 4203] [depth= 4] . ( 2 sec) [ -16491.0339] [ 4209] [depth= 12] . ( 2 sec) [ -16437.3854] [ 4195] [depth= 1] . ( 2 sec) [ -16290.4889] [ 4169] [depth= 7] . ( 2 sec) [ -15739.4891] [ 4068] [depth= 3] . ( 2 sec) [ -15653.4828] [ 4015] [depth= 10] . ( 2 sec) [ -15583.8371] [ 3996] [depth= 1] . ( 3 sec) [ -15343.1254] [ 3955] [depth= 9] . ( 3 sec) [ -15216.3307] [ 3885] [depth= 1] . ( 3 sec) [ -14914.8154] [ 3791] [depth= 14] . ( 3 sec) [ -14712.8056] [ 3739] [depth= 4] . ( 3 sec) [ -14437.3253] [ 3718] [depth= 9] . ( 3 sec) [ -14385.2187] [ 3697] [depth= 7] . ( 3 sec) [ -13968.9222] [ 3561] [depth= 3] . ( 3 sec) [ -13750.2837] [ 3529] [depth= 3] . ( 3 sec) [ -13437.2134] [ 3364] [depth= 3] . ( 3 sec) [ -13368.1673] [ 3334] [depth= 2] . ( 3 sec) [ -13159.9426] [ 3262] [depth= 5] . ( 3 sec) [ -12891.3193] [ 3204] [depth= 3] . ( 3 sec) [ -12881.6009] [ 3202] [depth= 1] . ( 3 sec) [ -12770.2093] [ 3157] [depth= 7] . ( 3 sec) [ -12677.5888] [ 3088] [depth= 4] . ( 3 sec) [ -12340.4853] [ 3069] [depth= 2] . ( 3 sec) [ -12306.2783] [ 3059] [depth= 1] . ( 3 sec) [ -12203.7061] [ 3016] [depth= 8] . ( 4 sec) [ -12147.2062] [ 2996] [depth= 2] . ( 4 sec) [ -12061.4669] [ 2966] [depth= 2] . ( 4 sec) [ -12012.3817] [ 2957] [depth= 6] . ( 4 sec) [ -11910.5945] [ 2953] [depth= 2] . ( 4 sec) [ -11849.8324] [ 2921] [depth= 1] . ( 4 sec) [ -11832.7143] [ 2917] [depth= 7] . ( 4 sec) [ -11799.5349] [ 2908] [depth= 1] . ( 4 sec) [ -11798.1247] [ 2897] [depth= 8] . ( 4 sec) [ -11780.9978] [ 2910] [depth= 1] . ( 4 sec) [ -11749.0385] [ 2911] [depth= 1] . ( 4 sec) [ -11672.1821] [ 2859] [depth= 1] . ( 4 sec) [ -11640.0818] [ 2847] [depth= 1] . ( 4 sec) [ -11636.5821] [ 2851] [depth= 1] . ( 4 sec) [ -11582.5629] [ 2836] [depth= 5] . ( 4 sec) [ -11566.1766] [ 2803] [depth= 1] . ( 4 sec) [ -11471.7863] [ 2749] [depth= 2] . ( 4 sec) [ -11456.4937] [ 2752] [depth= 1] . ( 5 sec) [ -11453.1113] [ 2748] [depth= 1] . ( 5 sec) [ -11452.1052] [ 2745] [depth= 1] . ( 5 sec) [ -11422.1241] [ 2743] [depth= 1] . ( 5 sec) [ -11366.4141] [ 2733] [depth= 3] . ( 5 sec) [ -11366.1319] [ 2734] [depth= 1] . ( 5 sec) [ -11348.5563] [ 2720] [depth= 1] . ( 5 sec) [ -11329.5824] [ 2719] [depth= 1] . ( 5 sec) [ -11312.0483] [ 2710] [depth= 1] . ( 5 sec) [ -11309.7576] [ 2715] [depth= 1] . ( 5 sec) [ -11117.9534] [Branch lengths ] . ( 6 sec) [ -11114.9295] [GTR parameters ] . ( 6 sec) [ -11064.6980] [Alpha ][ 0.982261] . ( 6 sec) [ -11064.2214] [ 2713] [depth= 1] . ( 6 sec) [ -10957.6483] [ 2678] [depth= 5] . ( 6 sec) [ -10938.8040] [ 2647] [depth= 1] . ( 6 sec) [ -10938.5504] [ 2651] [depth= 2] . ( 7 sec) [ -10929.3018] [ 2628] [depth= 1] . ( 7 sec) [ -10927.4672] [ 2630] [depth= 1] . ( 7 sec) [ -10907.4274] [ 2628] [depth= 5] . ( 7 sec) [ -10906.7095] [ 2624] [depth= 1] . ( 7 sec) [ -10902.4197] [ 2631] [depth= 1] . ( 7 sec) [ -10871.5902] [ 2628] [depth= 1] . ( 8 sec) [ -10869.2651] [ 2592] [depth= 2] . ( 8 sec) [ -10865.7514] [ 2590] [depth= 1] . ( 8 sec) [ -10860.8126] [ 2595] [depth= 1] . ( 8 sec) [ -10859.9676] [ 2594] [depth= 2] . ( 8 sec) [ -10854.4723] [ 2589] [depth= 2] . ( 8 sec) [ -10842.8070] [ 2589] [depth= 4] . ( 8 sec) [ -10842.2670] [ 2591] [depth= 1] . ( 9 sec) [ -10840.9373] [ 2593] [depth= 1] . ( 9 sec) [ -10837.9723] [ 2591] [depth= 1] . ( 9 sec) [ -10836.3599] [ 2591] [depth= 1] . ( 9 sec) [ -10833.4307] [ 2587] [depth= 2] . ( 9 sec) [ -10832.6197] [ 2588] [depth= 1] . ( 9 sec) [ -10831.8389] [ 2587] [depth= 1] . ( 9 sec) [ -10828.7870] [ 2589] [depth= 1] . ( 10 sec) [ -10808.1445] [Branch lengths ] . ( 10 sec) [ -10807.8028] [GTR parameters ] . ( 10 sec) [ -10805.7600] [Alpha ][ 1.126705] . ( 10 sec) [ -10805.7061] [ 2582] [depth= 1] . ( 11 sec) [ -10805.6554] [ 2585] [depth= 1] . ( 12 sec) [ -10804.9907] [ 2582] [depth= 1] . ( 12 sec) [ -10804.8613] [ 2579] [depth= 1] . ( 12 sec) [ -10803.8225] [ 2583] [depth= 1] . ( 14 sec) [ -10801.6317] [Branch lengths ] . ( 14 sec) [ -10801.6267] [GTR parameters ] . ( 14 sec) [ -10801.6126] [Alpha ][ 1.139980] . ( 17 sec) [ -10801.1323] [Branch lengths ] . ( 39 sec) [ -10801.0474] [Branch lengths ] . ( 39 sec) [ -10801.0474] [Topology ] . ( 40 sec) [ -10800.8079] [Topology ] . ( 41 sec) [ -10800.7473] [Topology ] . ( 42 sec) [ -10800.7324] [Topology ] . ( 43 sec) [ -10800.7268] [Topology ] . ( 44 sec) [ -10800.7246] [Topology ] . ( 44 sec) [ -10800.7236] [Topology ] . ( 45 sec) [ -10800.7200] [GTR parameters ] . ( 45 sec) [ -10800.7197] [Alpha ][ 1.142014] . ( 45 sec) [ -10800.7197] [Topology ] . ( 46 sec) [ -10800.7191] [Topology ] . ( 46 sec) [ -10800.7191] [GTR parameters ] . ( 46 sec) [ -10800.7191] [Alpha ][ 1.142014] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10800.719138. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10897.223759 . ( 0 sec) [ -10895.0531] [GTR parameters ] . ( 1 sec) [ -10892.5292] [Alpha ][ 1.177564] . ( 1 sec) [ -10892.5292] [Topology ] . ( 1 sec) [ -10821.8961] [Topology ] . ( 2 sec) [ -10809.2564] [Topology ] . ( 3 sec) [ -10804.6495] [Topology ] . ( 4 sec) [ -10802.5218] [Topology ] . ( 5 sec) [ -10801.6487] [Topology ] . ( 6 sec) [ -10801.2787] [Topology ] . ( 7 sec) [ -10801.0902] [Topology ] . ( 7 sec) [ -10800.9891] [Topology ] . ( 8 sec) [ -10800.9333] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.902207 . ( 16 sec) [ -10800.8556] [GTR parameters ] . ( 16 sec) [ -10800.7768] [Alpha ][ 1.146085] . ( 16 sec) [ -10800.7768] [Topology ] . ( 17 sec) [ -10800.7500] [Topology ] . ( 18 sec) [ -10800.7373] [Topology ] . ( 19 sec) [ -10800.7301] [Topology ] . ( 19 sec) [ -10800.7259] [Topology ] . ( 20 sec) [ -10800.7235] [Topology ] . ( 21 sec) [ -10800.7221] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.722117 . ( 28 sec) [ -10800.7220] [GTR parameters ] . ( 28 sec) [ -10800.7210] [Alpha ][ 1.142439] . ( 28 sec) [ -10800.7210] [Topology ] . ( 29 sec) [ -10800.7200] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.720028 . ( 36 sec) [ -10800.7200] [GTR parameters ] . ( 36 sec) [ -10800.7200] [Alpha ][ 1.142439] . ( 36 sec) [ -10800.7200] [Topology ] . ( 37 sec) [ -10800.7195] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 51 sec) [ -10895.0531] [GTR parameters ] . ( 51 sec) [ -10892.5292] [Alpha ][ 1.177564] . ( 51 sec) [ -10890.2018] [ 2589] [depth= 1] . ( 51 sec) [ -10888.2818] [ 2586] [depth= 1] . ( 51 sec) [ -10887.8184] [ 2585] [depth= 1] . ( 52 sec) [ -10882.7191] [ 2586] [depth= 1] . ( 52 sec) [ -10881.9989] [ 2585] [depth= 1] . ( 52 sec) [ -10873.6034] [ 2591] [depth= 1] . ( 52 sec) [ -10869.0209] [ 2585] [depth= 1] . ( 52 sec) [ -10865.5116] [ 2586] [depth= 1] . ( 53 sec) [ -10865.2345] [ 2586] [depth= 1] . ( 53 sec) [ -10865.0865] [ 2588] [depth= 1] . ( 53 sec) [ -10864.0226] [ 2586] [depth= 1] . ( 53 sec) [ -10859.4464] [ 2591] [depth= 4] . ( 53 sec) [ -10858.3842] [ 2592] [depth= 2] . ( 53 sec) [ -10854.5228] [ 2596] [depth= 1] . ( 53 sec) [ -10853.6309] [ 2597] [depth= 1] . ( 53 sec) [ -10852.0951] [ 2596] [depth= 1] . ( 54 sec) [ -10849.3884] [ 2592] [depth= 2] . ( 54 sec) [ -10844.2782] [ 2592] [depth= 1] . ( 54 sec) [ -10838.6564] [ 2584] [depth= 1] . ( 54 sec) [ -10837.5929] [ 2587] [depth= 1] . ( 54 sec) [ -10837.3106] [ 2591] [depth= 1] . ( 54 sec) [ -10837.1915] [ 2594] [depth= 1] . ( 54 sec) [ -10806.9055] [Branch lengths ] . ( 55 sec) [ -10806.8395] [GTR parameters ] . ( 55 sec) [ -10806.7109] [Alpha ][ 1.136825] . ( 56 sec) [ -10806.5491] [ 2599] [depth= 1] . ( 58 sec) [ -10806.4548] [ 2602] [depth= 1] . ( 59 sec) [ -10804.4028] [Branch lengths ] . ( 59 sec) [ -10804.4008] [GTR parameters ] . ( 59 sec) [ -10804.3998] [Alpha ][ 1.133248] . ( 60 sec) [ -10804.3106] [ 2599] [depth= 1] . ( 64 sec) [ -10803.8385] [Branch lengths ] . ( 64 sec) [ -10803.8381] [GTR parameters ] . ( 64 sec) [ -10803.8381] [Alpha ][ 1.133248] . ( 78 sec) [ -10803.5412] [ 2615] [depth= 1] . ( 79 sec) [ -10803.3886] [ 2610] [depth= 1] . ( 81 sec) [ -10802.8064] [ 2608] [depth= 3] . ( 82 sec) [ -10802.4955] [ 2607] [depth= 1] . ( 82 sec) [ -10802.4667] [ 2589] [depth= 1] . ( 85 sec) [ -10802.3605] [ 2601] [depth= 2] . ( 85 sec) [ -10801.3581] [Branch lengths ] . ( 85 sec) [ -10801.3437] [GTR parameters ] . ( 85 sec) [ -10801.3405] [Alpha ][ 1.139483] . ( 101 sec) [ -10801.1752] [ 2594] [depth= 1] . ( 107 sec) [ -10800.8665] [Branch lengths ] . ( 107 sec) [ -10800.8657] [GTR parameters ] . ( 107 sec) [ -10800.8657] [Alpha ][ 1.140622] . ( 107 sec) [ -10800.8657] [Topology ] . ( 108 sec) [ -10800.8311] [Topology ] . ( 109 sec) [ -10800.8184] [Topology ] . ( 110 sec) [ -10800.8127] [Topology ] . ( 111 sec) [ -10800.8101] [Topology ] . ( 112 sec) [ -10800.8088] [Topology ] . ( 112 sec) [ -10800.8083] [Topology ] . ( 113 sec) [ -10800.8082] [GTR parameters ] . ( 113 sec) [ -10800.8082] [Alpha ][ 1.139482] . ( 113 sec) [ -10800.8082] [Topology ] . ( 113 sec) [ -10800.8079] [Topology ] . ( 114 sec) [ -10800.8079] [GTR parameters ] . ( 114 sec) [ -10800.8079] [Alpha ][ 1.139482] . Checking for NNIs, optimizing five branches... . ( 120 sec) [ -10800.7224] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10800.719503 . Log likelihood obtained after SPR moves : -10800.722354 . Log likelihood of the current tree: -10800.719503. . Printing the most likely tree in file 'data29.phy_phyml_tree.txt'... . Best log likelihood : -10800.719026 . Time used 0h2m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo